I am currently running the following 2 setups.

Intel Xeon X5670
Intel DX58SO (x58)

Intel I7 980
MSI Big Bang X-Power (x58)

I am using IOMMU along with VFIO to passthrough a VGA card on both of my setups. Everything worked fine till kernel 4.1, but after the introduction of "iommu/vt-d: Make root entry visible for hardware right after allocation", both the boards no longer boot with "intel_iommu=on" commandline parameter.

The logs show the following:
DMAR: RMRR base: 0x000000bf7e8000 end: 0x000000bf7fffff
DMAR: ATSR flags: 0x0
DMAR: dmar0: Using Queued invalidation
------------[ cut here ]------------
WARNING: CPU: 4: PID: 1 at /home/dhiru1602/linux-git/kernel/watchdog.c:311 watchdog_overflow_callback+0x79/0xa0()
Watchdog detected hard LOCKUP on cpu 4
Modules Linked in:
CPU: 4 PID: 1 Comm: swapper/0 Tainted: G              I       4.2.0-iommu-test

The kernel panic occurs very early in the boot process and I was not able to grab the full kernel panic log. 

I have reverted the patch and recompiled the kernel. I was able to boot fine on both the boards with intel_iommu=on and I was able to see the IOMMU groups.

On a sidenote, Both the boards have broken interrupt remapping and the vendors have not provided BIOS updates to fix this problem. There was a report for the Intel board made on the Intel Community Forums here: https://communities.intel.com/thread/44752 but there hasn't been an updated BIOS released by Intel to fix this issue.

Please let me know if more information is needed to diagnose this issue.
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Regards,
Dheeraj CVR.